Polina Kobchikova

6 Questions 10 Answers 0 Followers

Questions related from Polina Kobchikova

Why can't ORCA read the file properly while doing NEB-TS?

So, my input file: ! PBEh-3c TightSCF Mass2016 NEB-TS FREQ %NEB NEB_END_XYZFILE "angle.xyz" NIMAGES 20 END * XYZFILE 0 1 linear.xyz I can swap files with structures, the error will always be...

14 January 2025 1,506 7 View

How to evaluate adsorption of MOFs using molecular dynamics?

We are going to study some MOFs, but I have no experience at all. I did some calculations using GROMACS, so now I have the following questions: - as I understand, it is possible to evaluate the...

04 October 2024 2,184 2 View

How to effectively compare tomograms of plant roots?

I was given neutron tomograms of plant roots. I don't want to analyze them manually, whether they are different or not. For example, counting the number of nodes myself would be problematic. I saw...

26 August 2024 7,035 2 View

How to prepare a molecule for molecular dynamics calculations?

If I want to calculate molecular dynamics (Gromacs), do I first need to optimize the geometry of the molecule? For example, I first draw the molecule in Avogadro, and then what? I guess I can't...

29 July 2024 1,043 3 View

Why Orca calculations take too loong?

Hello! I am trying to calculate the sumatriptan molecule, but it has been counting for five days and it does not stop. It seems to me that it is too long and I am doing something wrong. Please...

26 July 2024 3,452 5 View

ORCA. What does this error mean: cleanup molecule is Linear but not aligned to z-axis?

Dear researchers, Here is my input file: # avogadro generated ORCA input file # Basic Mode # ! RHF SP def2-SVP Opt Freq MORead #! BP RI OPT FREQ def2-SVP def2/J MORead %moinp "co2.gbw" *...

13 June 2024 1,852 6 View